Zhang L.,Shanghai JiaoTong University |
Yu S.,Shanghai Academy of Agricultural science |
Zuo K.,Shanghai JiaoTong University |
Luo L.,Shanghai Academy of Agricultural science |
Tang K.,Shanghai JiaoTong University
PLoS ONE | Year: 2012
Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice. © 2012 Zhang et al.
Song S.,Shanghai Academy of Agricultural science |
Liu N.,Shanghai Academy of Agricultural science |
Zhao Z.,Shanghai Academy of Agricultural science |
Njumbe Ediage E.,Ghent University |
And 4 more authors.
Analytical Chemistry | Year: 2014
A new lateral flow immunoassay (LFA) is proposed for qualitative and/or semiquantitative determination of aflatoxin B1 (AFB1), zearalenone (ZEA), deoxynivalenol (DON), and their analogues (AFs, ZEAs, DONs) in cereal samples. Each of the mycotoxin specific antibody was class specific and there was no cross reactivity to other groups of compounds. The visual limits of detection (vLOD) of the strip were 0.03, 1.6, and 10 μg/kg for AFB1, ZEA and DON, respectively. The calculated limits of detection (cLOD) were 0.05, 1, and 3 μg/kg, respectively. Meanwhile the cutoff values were achieved at 1, 50, and 60 μg/kg for AFB1, ZEA and DON, respectively. Recoveries ranged from 80% to 122% and RSD from 5% to 20%. Both the vLOD and cLOD for the three mycotoxins were lower than the EU maximum levels. Analysis of naturally contaminated maize samples resulted in a good agreement between the multiplex LFA and LC-MS/MS (100% for DONs and AFs, and 81% for ZEAs). Careful analysis of the results further explained the general overestimation of LFA compared to chromatographic methods for quantification of mycotoxins. © 2014 American Chemical Society.
Zhang A.-Q.,Zhejiang University of Technology |
Fu L.,Zhejiang University of Technology |
Xu M.,Zhejiang University of Technology |
Sun P.-L.,Zhejiang University of Technology |
Zhang J.-S.,Shanghai Academy of Agricultural science
Carbohydrate Polymers | Year: 2012
A new heteropolysaccharide (HEPF4), with a molecular weight of 2.03 × 10 4 Da as determined by high-performance liquid chromatography (HPLC), was obtained from the fruiting bodies of Hericium erinaceus. It is composed of 3-O-methylrhamnose, l-fucose, d-galactose and d-glucose in the ratio of 0.12:1.00:3.27:0.28. Its chemical structure was characterized by sugar and methylation analysis, along with 1H and 13C NMR spectroscopy, including NOESY and HMBC experiments for linkage and sequence analysis. The polysaccharide is composed of a tetrasaccharide repeating unit (described in the results section). HEPF4 also contains a minor proportion of glucose and 3-O-methylrhamnose which is believed to terminate the polymer main chain. © 2011 Elsevier Ltd. All rights reserved.
Liu L.,Shanghai Academy of Agricultural science |
Free S.J.,State University of New York at Buffalo
Molecular Plant Pathology | Year: 2016
We used a proteomic analysis to identify cell wall proteins released from Sclerotinia sclerotiorum hyphal and sclerotial cell walls via a trifluoromethanesulfonic acid (TFMS) digestion. Cell walls from hyphae grown in Vogel's glucose medium (a synthetic medium lacking plant materials), from hyphae grown in potato dextrose broth and from sclerotia produced on potato dextrose agar were used in the analysis. Under the conditions used, TFMS digests the glycosidic linkages in the cell walls to release intact cell wall proteins. The analysis identified 24 glycosylphosphatidylinositol (GPI)-anchored cell wall proteins and 30 non-GPI-anchored cell wall proteins. We found that the cell walls contained an array of cell wall biosynthetic enzymes similar to those found in the cell walls of other fungi. When comparing the proteins in hyphal cell walls grown in potato dextrose broth with those in hyphal cell walls grown in the absence of plant material, it was found that a core group of cell wall biosynthetic proteins and some proteins associated with pathogenicity (secreted cellulases, pectin lyases, glucosidases and proteases) were expressed in both types of hyphae. The hyphae grown in potato dextrose broth contained a number of additional proteins (laccases, oxalate decarboxylase, peroxidase, polysaccharide deacetylase and several proteins unique to Sclerotinia and Botrytis) that might facilitate growth on a plant host. A comparison of the proteins in the sclerotial cell wall with the proteins in the hyphal cell wall demonstrated that sclerotia formation is not marked by a major shift in the composition of cell wall protein. We found that the S. sclerotiorum cell walls contained 11 cell wall proteins that were encoded only in Sclerotinia and Botrytis genomes. © 2015 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd
Zhang J.,University of Shanghai for Science and Technology |
Zhang J.,Shanghai Academy of Agricultural science
Critical Reviews in Biotechnology | Year: 2015
Filamentous fungi play an important role not only in the bio-manufacturing of value-added products, but also in bioenergy and environmental research. The bioprocess manipulation of filamentous fungi is more difficult than that of other microbial species because of their different pellet morphologies and the presence of tangled mycelia under different cultivation conditions. Fungal pellets, which have the advantages of harvest ease, low fermentation broth viscosity and high yield of some proteins, have been used for a long time. Many attempts have been made to establish the relationship between pellet and product yield using quantitative approaches. Fungal pellet formation is attributed to the combination of electrostatic interactions, hydrophobicity and specific interactions from spore wall components. Electrostatic interactions result from van der Waals forces and negative charge repulsion from carboxyl groups in the spore wall structure. Electrostatic interactions are also affected by counter-ions (cations) and the physiologic conditions of spores that modify the carboxyl groups. Fungal aggregates are promoted by the hydrophobicity generated by hydrophobins, which form a hydrophobic coat that covers the spore. The specific interactions of spore wall components contribute to spore aggregation through salt bridging. A model of spore aggregation was proposed based on these forces. Additionally, some challenges were addressed, including the limitations of research techniques, the quantitative determination of forces and the complex information of biological systems, to clarify the mechanism of fungal pellet formation. © 2015 Taylor & Francis.
Chen Z.W.,Shanghai Academy of Agricultural science
Genetics and molecular research : GMR | Year: 2012
We analyzed the genetic diversity of 115 barley germplasms, including 112 landraces and three new barley cultivars grown in the Shanghai region, using a set of 11 SSR markers. Sixty-six alleles were observed at the 11 SSR loci, ranged from three to ten, with a mean of six alleles per locus. The polymorphism information content ranged from 0.568 to 0.853, with a mean of 0.732, indicating considerable genetic variation in barley in the Shanghai area. Clustering analysis indicated that these barley accessions could be divided into two categories (A and B). Ninety-seven six-rowed barley cultivars were classified in the A category; sixteen two-rowed and two six-rowed barley cultivars were classified in the B category. This demonstrated genetic differences between two-rowed and six-rowed barley varieties. In addition, we found that the three new barley cultivars are closely related.
Shuai J.J.,Shanghai Academy of Agricultural science
Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji | Year: 2011
As one of the persistent organic pollutants, polychlorinated biphenyls are harmful to the environment and humans. Biodegradation is the most potential way to remove PCBs. Biodegradation can mainly be divided into microbial degradation, phytoremediation, plant and microbial combined remediation. Here, we introduced isolation of the PCBs-degrading strains, cloning and modification of the related degradation genes. Additionally, on the other hand, the natural remediation of plant, plant and microbial combined remediation, plant transgenic remediation were described.
Halford N.G.,Rothamsted Research |
Curtis T.Y.,Rothamsted Research |
Chen Z.,Shanghai Academy of Agricultural science |
Huang J.,Shanghai Academy of Agricultural science
Journal of Experimental Botany | Year: 2015
The effects of abiotic stresses and crop management on cereal grain composition are reviewed, focusing on phytochemicals, vitamins, fibre, protein, free amino acids, sugars, and oils. These effects are discussed in the context of nutritional and processing quality and the potential for formation of processing contaminants, such as acrylamide, furan, hydroxymethylfurfuryl, and trans fatty acids. The implications of climate change for cereal grain quality and food safety are considered. It is concluded that the identification of specific environmental stresses that affect grain composition in ways that have implications for food quality and safety and how these stresses interact with genetic factors and will be affected by climate change needs more investigation. Plant researchers and breeders are encouraged to address the issue of processing contaminants or risk appearing out of touch with major end-users in the food industry, and not to overlook the effects of environmental stresses and crop management on crop composition, quality, and safety as they strive to increase yield. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved.
Yi J.,Shanghai Academy of Agricultural science |
Liu C.,Shanghai Academy of Agricultural science
PLoS ONE | Year: 2011
Background: DNAzymes are DNA molecules that can directly cleave cognate mRNA, and have been developed to silence gene expression for research and clinical purposes. The advantage of DNAzymes over ribozymes is that they are inexpensive to produce and exhibit good stability. The "10-23 DNA enzyme" is composed of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of approximately eight nucleotides in each direction, which provides the complementary sequence required for specific binding to RNA substrates. However, these eight nucleotides might not afford sufficient binding energy to hold the RNA substrate along with the DNAzyme, which would interfere with the efficiency of the DNAzyme or cause side effects, such as the cleavage of non-cognate mRNAs. Methodology: In this study, we inserted a nonpairing bulge at the 5′ end of the "10-23 DNA enzyme" to enhance its efficiency and specificity. Different sizes of bulges were inserted at different positions in the 5′ end of the DNAzyme. The non-matching bulge will avoid strong binding between the DNAzyme and target mRNA, which may interfere with the efficiency of the DNAzyme. Conclusions: Our novel DNAzyme constructs could efficiently silence the expression of target genes, proving a powerful tool for gene silencing. The results showed that the six oligo bulge was the most effective when the six oligo bulge was 12-15 bp away from the core catalytic domain. © 2011 Yi, Liu.
Du X.,Liaocheng University |
Mu H.,Liaocheng University |
Zhou S.,Shanghai Academy of Agricultural science |
Zhang Y.,Liaocheng University |
Zhu X.,Liaocheng University
International Journal of Biological Macromolecules | Year: 2013
Three water-soluble polysaccharide fractions (IOP40, IOP60 and IOP80) were isolated by using different concentrations of alcohol precipitation from Inonotus obliquus sclerotia. Their physicochemical properties, including total sugar content, protein content, monosaccharide composition and percentage were analyzed. And their in vitro antioxidant capacities were investigated in terms of reducing power assay and scavenging of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals, hydroxyl radicals, superoxide anion radicals and hydrogen peroxide (H2O2). In general, three polysaccharide fractions exhibited increasing antioxidant activity with increasing concentration at the ranges of tested dosage. The orders of reducing power, DPPH-scavenging capacity, H2O2-scavenging capacity, and hydroxyl-scavenging activity were all IOP60>IOP40>IOP80. These findings demonstrated that three polysaccharide fractions extracted from I. obliquus, especially IOP60, could be employed as natural ingredients in functional food and pharmaceutical industry to alleviate the oxidative stress. © 2013 Elsevier B.V.